A report by New Zealand's top scientist has urged politicians to address freshwater issues, which he says are clearly linked to intensive farming and urbanisation.

Professor Sir Peter Gluckman, chief science advisor to the prime minister, has released a report analysing the health of New Zealand's freshwater based on existing science and data.

It found clear evidence the freshwater estate was under pressure in terms of both water quality and quantity. There was a link between farming and declining water quality in pastoral areas, and contamination of urban waterways by expanding cities.